Mitochondria in the Layer 2/3 Volume
Visualization and analysis of mitochondria by voxel (volume) and counts per cell.
A special thanks to Nick Turner for his advice and help. Read Nick and his Microns Consortium colleagues’ Cell paper Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity for more details.
See the Microns explorer page at the Allen Brain Institute for more details, terms and conditions.
An astrocyte containing several large contiguous mitochondria in the layer 2/3 volume.
Summary Presentation
View the Mitochondria summary presentation file, with lots of visualization examples of mitchondria in neurons and glia.
Contents
Jupyter Notebook files
The main analysis was conducted using mito_voxel_analysis_vasc_removed.ipynb.
This notebook removes the vascular cells and all the partial processes
from cells where the soma is not located in the volume. The cell
subtypes table 220309_cell_type_classification.csv
was used to provide identifying information for the neuron or glial cell
of interest.
Use mito_voxel_analysis_entire_table.ipynb
to look up mitochondria segmentation data on any cell id in the volume.
This includes a substantial number of partial processes from cells where
the soma is not located in the volume.
Note: The mitochondria table is too large to place on GitHub. You will need to download this file to your local computer in order to run these Anaconda notebook files.
A selection of interesting visualizations
See the summary presentation for more examples and additional commentary.
The largest mitochondrion in the volume
View in neuroglancer.
Note that the load time is long.
The largest contiguous mitochondria by voxel size is within an astrocyte in the Layer 2/3 volume.
The largest contiguous mitochondrion in the Layer 2/3 volume.
The neuron with the largest contiguous mitochondrion in the volume
View in neuroglancer.
This excitatory pyramidal neuron has the largest contiguous mitochondrion by voxels (volume) for a neuron in the Layer 2/3 volume.
The largest contiguous mitochondrion with a neuron in the layer 2/3 volume.
The neuron with the highest number of mitochondria by count
View in neuroglancer.
The hyperlink is so large that I had to create a Google Doc to contain it. Clicking on the hyperlink will open Neuroglancer; please note that the load time is very long.
This inhibitory basket neuron (648518346349539215) has 3213
mitochondria and is also the neuron with the most pre-synaptic contacts
in the volume. See most_synapses
folder for visualization of the synaptic sites on this neuron.
Inhibitory basket neuron with the highest number of mitochondria in the layer 2/3 volume.